# HG changeset patch # User bgruening # Date 1426845915 14400 # Node ID 424b0639008438aec051f763879283c09b881299 # Parent e861182a8034a266ce8e3e95209a55790c804ec1 Uploaded diff -r e861182a8034 -r 424b06390084 find_subsequences.py --- a/find_subsequences.py Fri Mar 20 04:15:42 2015 -0400 +++ b/find_subsequences.py Fri Mar 20 06:05:15 2015 -0400 @@ -33,7 +33,7 @@ """ bed_template = '%s\t%s\t%s\t%s\t%s\t%s\n' for match in re.finditer( str(pattern), str(sequence.seq) ): - outfile.write(bed_template % (sequence.id, match.start(), match.end(), sequence.name, '', strand)) + outfile.write(bed_template % (sequence.id, match.start(), match.end(), sequence.description, '', strand)) def complex_pattern_search(sequence, pattern, outfile, strand='+'): @@ -45,7 +45,7 @@ matches = nt_search(str(sequence.seq), pattern) bed_template = '%s\t%s\t%s\t%s\t%s\t%s\n' for match in matches[1:]: - outfile.write(bed_template % (sequence.id, match, match+l, sequence.name, '', strand) ) + outfile.write(bed_template % (sequence.id, match, match+l, sequence.description, '', strand) ) if __name__ == "__main__": diff -r e861182a8034 -r 424b06390084 find_subsequences.xml --- a/find_subsequences.xml Fri Mar 20 04:15:42 2015 -0400 +++ b/find_subsequences.xml Fri Mar 20 06:05:15 2015 -0400 @@ -27,218 +27,218 @@ - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + - - - + + - - - - - - - - - - - + + + + + + + + + + + - - - - - - - - - - - - - - + + - - - - - - - - - - - + + - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - + + + + + + + + + + + + - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + + + + + + + - - - - - - - - - - - - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - - - - - - - - - + + + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - -